{"title"=>"TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements", "type"=>"journal", "authors"=>[{"first_name"=>"Kamila", "last_name"=>"Maliszewska-Olejniczak", "scopus_author_id"=>"56768238800"}, {"first_name"=>"Julita", "last_name"=>"Gruchota", "scopus_author_id"=>"56768032900"}, {"first_name"=>"Robert", "last_name"=>"Gromadka", "scopus_author_id"=>"6603472660"}, {"first_name"=>"Cyril", "last_name"=>"Denby Wilkes", "scopus_author_id"=>"55440882900"}, {"first_name"=>"Olivier", "last_name"=>"Arnaiz", "scopus_author_id"=>"15058857300"}, {"first_name"=>"Nathalie", "last_name"=>"Mathy", "scopus_author_id"=>"56767959500"}, {"first_name"=>"Sandra", "last_name"=>"Duharcourt", "scopus_author_id"=>"6603204570"}, {"first_name"=>"Mireille", "last_name"=>"Bétermier", "scopus_author_id"=>"6701610390"}, {"first_name"=>"Jacek K.", "last_name"=>"Nowak", "scopus_author_id"=>"36625954300"}], "year"=>2015, "source"=>"PLoS Genetics", "identifiers"=>{"isbn"=>"0000871400", "pmid"=>"26177014", "doi"=>"10.1371/journal.pgen.1005383", "issn"=>"15537404", "pui"=>"605567896", "sgr"=>"84938818552", "scopus"=>"2-s2.0-84938818552"}, "id"=>"82494b3a-a215-318c-826c-e3917ad9fabe", "abstract"=>"Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs) in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline) nucleus, while the old somatic nucleus degenerates. In the ciliate Paramecium tetraurelia, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs). Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in P. tetraurelia genome. Using RNA interference, we showed that TFIIS4, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon TFIIS4 RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in Paramecium, and establishes for the first time a specific role of TFIIS in non-coding transcription in eukaryotes.", "link"=>"http://www.mendeley.com/research/tfiisdependent-noncoding-transcription-regulates-developmental-genome-rearrangements", "reader_count"=>20, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>2, "Student > Bachelor"=>3, "Professor"=>1, "Student > Postgraduate"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>2, "Student > Bachelor"=>3, "Professor"=>1, "Student > Postgraduate"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>13, "Neuroscience"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}}, "reader_count_by_country"=>{"Poland"=>1}, "group_count"=>3}

{"files"=>["https://ndownloader.figshare.com/files/2177039"], "description"=>"<p>For each transgene, representative images illustrate different developmental stages observed in a population of cells derived from a single injected caryonide. Panels a, f, l and s show vegetative cells (note that one vegetative cell is also present in the middle of panel b and on the left of panel h). All other panels show successive stages of autogamy: panels g, m and t–meiotic crescent stage; panels b and n–first meiotic division; panels h and u–cells with 8 haploid nuclei resulting from meiosis II; panels c, i, o and v–fragmentation of old MAC; panels d, j, p, and w–early MAC development; panels e, k, r and x–late MAC development. Note that panel b contains not only one meiotic cell (on the left) but also one vegetative cell (in the middle) and two cells with their fragmented old MAC (at the top and on the right). In all panels, white arrows point at MICs (some were omitted when MICs were not clearly distinguishable by DAPI staining), white arrowheads indicate new MACs. Yellow arrowheads in panels i and o point to division products of the zygotic nucleus. (A) A GFP-TFIIS1a fusion localizes to old, then new MACs. (B) A GFP-TFIIS2a fusion localizes to old MAC during meiosis, then to new MACs and is present in meiotic MICs. (C) As in B for a GFP-TFIIS3 fusion. GFP-TFIIS3 cannot be seen in division products of the zygotic nucleus. (D) A GFP-TFIIS4 fusion is essentially restricted to the new MACs specifically during early MAC development. Very weak GFP signal is visible in the old MAC during meiosis.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484258, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Localization_of_GFP_fusion_proteins_forTFIIS1a_TFIIS2a_TFIIS3_and_TFIIS4_/1484258", "title"=>"Localization of GFP fusion proteins forTFIIS1a, TFIIS2a, TFIIS3 and TFIIS4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}

{"files"=>["https://ndownloader.figshare.com/files/2177044"], "description"=>"<p>(A) PCR analysis of the excision of IESs located in the surface antigen gene <i>A</i><sup><i>51</i></sup> using primers located around each IES. In each panel, the larger fragment corresponds to the non-excised form (IES+), the smaller fragment to the excised form (IES-). Known maternally controlled IESs are labeled with an asterisk. The autogamy time-course experiment was performed using a strain harboring a somatic (macronuclear) deletion of part of surface antigen gene <i>A</i><sup><i>51</i></sup>, which overlaps 3 tested IESs – 51A1835, 51A4404, 51A2591 and partially 51A4578. In this experiment, we obtained 93% lethality in post-autogamous progeny of <i>TFIIS4</i>-silenced cells. (B) As in A for IESs located in other regions. The PCR products corresponding to each IES- form are amplified mostly from the fragments of the old MAC. Oligonucleotide sequences are listed in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005383#pgen.1005383.s013\" target=\"_blank\">S2 Table</a>. (C) IES retention scores calculated from the genome-wide sequencing of DNA extracted from purified nuclei of cells silenced for <i>TFIIS4</i> during an independent RNAi experiment (87% lethality in post-autogamous progeny). (D) Superimposed histogram of TFIIS4 retention scores for all IESs (dark blue) and for IESs that are significantly retained in TFIIS4-depleted cells (light blue). Around 25,000 IESs are not significantly affected by the inactivation of <i>TFIIS4</i> and a large fraction of IESs exhibits a retention score equal to 0. For TFIIS4-dependent IESs, retention scores are almost uniformly distributed between 0.1 and 0.7. (E) The graph shows a positive correlation between IES size and retention score in <i>TFIIS4</i> RNAi. The box plot displays the IES size distribution for all IESs and for each of <i>TFIIS4</i> retention score (RS) quartiles. The median retention score (horizontal line inside the box) and the first (top of box) and third (bottom of box) quartiles are shown. Range of RS for particular quartiles are as follows: Q1: [0–0.01[; Q2: [0.01–0.12[; Q3: [0.12–0.39[; Q4: [0.39–1.00]. The medians are significantly different between all the groups (p < 2e-40). (F) Venn diagram of significantly retained IESs after <i>TFIIS4</i>, <i>DCL5</i> or <i>DCL2/3</i> silencing. Almost all IESs that are dependent upon Dcl2/3 or Dcl5 for their excision are also dependent upon TFIIS4.</p>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484263, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005383.g004", "stats"=>{"downloads"=>0, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_IES_excision_in_TFIIS4_silenced_cells_/1484263", "title"=>"Analysis of IES excision in <i>TFIIS4</i>-silenced cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-15 04:07:52"}

{"files"=>["https://ndownloader.figshare.com/files/2177066", "https://ndownloader.figshare.com/files/2177067", "https://ndownloader.figshare.com/files/2177068", "https://ndownloader.figshare.com/files/2177069", "https://ndownloader.figshare.com/files/2177070", "https://ndownloader.figshare.com/files/2177071", "https://ndownloader.figshare.com/files/2177072", "https://ndownloader.figshare.com/files/2177073", "https://ndownloader.figshare.com/files/2177074", "https://ndownloader.figshare.com/files/2177075", "https://ndownloader.figshare.com/files/2177076", "https://ndownloader.figshare.com/files/2177077", "https://ndownloader.figshare.com/files/2177078", "https://ndownloader.figshare.com/files/2177080"], "description"=>"<div><p>Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs) in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline) nucleus, while the old somatic nucleus degenerates. In the ciliate <i>Paramecium tetraurelia</i>, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs). Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in <i>P</i>. <i>tetraurelia</i> genome. Using RNA interference, we showed that <i>TFIIS4</i>, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon <i>TFIIS4</i> RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in <i>Paramecium</i>, and establishes for the first time a specific role of TFIIS in non-coding transcription in eukaryotes.</p></div>", "links"=>[], "tags"=>["TFIIS 4", "RNA polymerase II transcriptional", "TFIIS 4 RNAi", "dna", "ies", "TFIIS elongation factor", "excision", "ncrna", "Ciliate Paramecium tetraurelia", "nucleus", "genome rearrangements", "Internal Eliminated Sequences"], "article_id"=>1484275, "categories"=>["Uncategorised"], "users"=>["Kamila Maliszewska-Olejniczak", "Julita Gruchota", "Robert Gromadka", "Cyril Denby Wilkes", "Olivier Arnaiz", "Nathalie Mathy", "Sandra Duharcourt", "Mireille Bétermier", "Jacek K. Nowak"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1005383.s001", "https://dx.doi.org/10.1371/journal.pgen.1005383.s002", "https://dx.doi.org/10.1371/journal.pgen.1005383.s003", "https://dx.doi.org/10.1371/journal.pgen.1005383.s004", "https://dx.doi.org/10.1371/journal.pgen.1005383.s005", "https://dx.doi.org/10.1371/journal.pgen.1005383.s006", "https://dx.doi.org/10.1371/journal.pgen.1005383.s007", "https://dx.doi.org/10.1371/journal.pgen.1005383.s008", "https://dx.doi.org/10.1371/journal.pgen.1005383.s009", "https://dx.doi.org/10.1371/journal.pgen.1005383.s010", "https://dx.doi.org/10.1371/journal.pgen.1005383.s011", "https://dx.doi.org/10.1371/journal.pgen.1005383.s012", "https://dx.doi.org/10.1371/journal.pgen.1005383.s013", "https://dx.doi.org/10.1371/journal.pgen.1005383.s014"], "stats"=>{"downloads"=>5, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TFIIS_Dependent_Non_coding_Transcription_Regulates_Developmental_Genome_Rearrangements_/1484275", "title"=>"TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-07-15 04:07:52"}